Clean the ambercup squash, cut off the ends, and remove the seeds. Cut the squash into bite-sized pieces. If you're using butternut squash, peel it first before cutting it into pieces.
Peel and roughly chop the onion. In a pan, heat 4 tablespoons of olive oil over low heat and sauté the onion and squash until soft. If you're using dried marjoram, add it now to allow the flavor to develop.
Once soft, puree half of the squash and onion mixture with the remaining 1 tablespoon of olive oil and the nutritional yeast flakes. If you're using fresh marjoram, add it now to be blended in. Use a food processor or an immersion blender for this step. The sauce should have the consistency of soft cream. If it's too thick, add a bit of water until it reaches your desired consistency.
Season the squash sauce with salt and pepper to taste.
If serving with pasta, cook the pasta al dente according to the package instructions. Toss the hot pasta with the squash sauce, mixing gently to coat.Serve topped with the remaining squash pieces, toasted cedar nuts (or pine nuts), fresh parsley (or marjoram), and a drizzle of olive oil.